SAXSdb — 7ule

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Coenzyme F420:L-glutamate ligase

Archaeoglobus fulgidus DSM 4304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GUANOSINE-5'-DIPHOSPHATE × 2 ;(2~{S})-2-[[(2~{S})-2-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[2,4,8-tris(oxidanylidene)-1,9-dihydropyrimido[4,5-b]quinolin-10-yl]pentoxy]phosphoryl]oxypropanoyl]amino]pentanedioic acid ; × 2 MANGANESE (II) ION × 4 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COFE_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–251； UniProt 1–249

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7ule
Deposition date deposition_date	2022-04-04
Structure title title	F420-1/GDP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus
Keywords keywords	ligase substrate complex, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7ule__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7ule__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ule__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	23.43 Å
Rg (electron density)	22.44 Å
Total Rg	23.15 Å
Atom count	3862
Residues	496
Excluded volume	68643 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ule__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Coenzyme F420:L-glutamate ligase
Molecular weight formula_weight	27423.6 kDa
EC 编号 ec_number	6.3.2.31,6.3.2.34
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2073

GAMRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL

Source Source

Source organism organism	Archaeoglobus fulgidus DSM 4304
NCBI taxonomy ID ncbi_taxonomy_id	224325
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	;(2~{S})-2-[[(2~{S})-2-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[2,4,8-tris(oxidanylidene)-1,9-dihydropyrimido[4,5-b]quinolin-10-yl]pentoxy]phosphoryl]oxypropanoyl]amino]pentanedioic acid ;
Molecular weight formula_weight	644.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

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Unit-cell length a length_a	69.082 Å
Unit-cell length b length_b	69.082 Å
Unit-cell length c length_c	92.352 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	48.896 Å
R factor r_factor	—
R_work r_work	0.2097
R_free r_free	0.2337

F420-1/GDP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus

1. Protein Identity and Related Structures Protein Identity & Related Structures

Coenzyme F420:L-glutamate ligase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7ule__assembly_1__model_1

7ule__assembly_1__model_1 | I(q)

7ule__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

F420-1/GDP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus

1. Protein Identity and Related Structures Protein Identity & Related Structures

Coenzyme F420:L-glutamate ligase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7ule__assembly_1__model_1

7ule__assembly_1__model_1 | I(q)

7ule__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)